Microarray Data Preprocessing: From Experimental Design to Differential Analysis

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Abstract

DNA microarray data preprocessing is of utmost importance in the analytical path starting from the experimental design and leading to a reliable biological interpretation. In fact, when all relevant aspects regarding the experimental plan have been considered, the following steps from data quality check to differential analysis will lead to robust, trustworthy results. In this chapter, all the relevant aspects and considerations about microarray preprocessing will be discussed. Preprocessing steps are organized in an orderly manner, from experimental design to quality check and batch effect removal, including the most common visualization methods. Furthermore, we will discuss data representation and differential testing methods with a focus on the most common microarray technologies, such as gene expression and DNA methylation.

Original languageEnglish
Title of host publicationMicroarray Data Analysis
EditorsGiuseppe Agapito
PublisherHumana Press
Pages79-100
Number of pages22
ISBN (Electronic)978-1-0716-1839-4
ISBN (Print)978-1-0716-1841-7
DOIs
Publication statusPublished - 2022
Publication typeA3 Part of a book or another research book

Publication series

NameMethods in Molecular Biology
Volume2401
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Batch effect
  • Differential analysis
  • DNA methylation
  • Experimental design
  • Gene expression
  • Microarray
  • Normalization
  • Omics data analysis
  • Preprocessing

Publication forum classification

  • Publication forum level 1

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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